Any author may explain the truths of a science or the methods of an art that are the property of the entire world and get a copyright in the work. That copyright, however, does not extend to the method or use of the system described. A system is simply not subject to copyright protection. To protect a system, the author would have to apply for a patent and meet the patent requirements.
This is where the method of operation language comes from in the EFF document. They are arguing that that API is a method of using the system.(java) They are arguing that you can't protect java by copyrighting the API. That it should be protected with patents instead.
The idea–expression divide differentiates between ideas and expression, and states that copyright protects only the original expression of ideas, and not the ideas themselves.
This came about in a court case where someone tried to copyright a book keeping form they invented. They were attempting to get copyright on the form because they failed to get a patent on it. The inventor carefully thought out how the book keeping form should look like. It was not a mere arrangement of facts or information. The courts rejected this argument. They did not want useful inventions covered by copyright when congress intended for them to be covered by patents. In 1975 congress updated the law to match what the Supreme court ruled.
existing in or caused by nature; not made or caused by humankind.
Dogs and GMO crops are artificial lifeforms. They were caused by humankind. If humans did not exists then dogs would not exist. Humans don't create anything from scratch. We always create using a mix of natural and artificial parts. Everything we create is artificial by definition.
Definition of artificial:
made or produced by human beings rather than occurring naturally, typically as a copy of something natural
Definition of supernatural
(of a manifestation or event) attributed to some force beyond scientific understanding or the laws of nature.
It's a naive, domestic operating system without any breeding, but I think you'll be amused by its presumption.